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Review: Oligonucleotide-based tools for studying zebrafish development.

Review: Oligonucleotide-based tools for studying zebrafish development. - Zebrafish Forum

Review: Oligonucleotide-based tools for studying zebrafish development. - Zebrafish Danio Rerio Forum. Discuss zebrafish, aquarium culture and molecular biology lab specimens.


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  #1  
Old 05-07-2010, 04:32 PM
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Default Review: Oligonucleotide-based tools for studying zebrafish development.



Shestopalov IA, Chen JK. [Only registered users see links. ] Zebrafish. 2010 Mar;7(1):31-40.
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Old 01-04-2012, 11:36 PM
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Default Re: Review: Oligonucleotide-based tools for studying zebrafish development.

Hello everyone ,
i need help regarding the in vivo application of morpholino in zebrafish. can you please refer me a paper or give me some information on that .

Thank you guys
Sunil
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Old 01-09-2012, 05:38 PM
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Default Re: Review: Oligonucleotide-based tools for studying zebrafish development.

If you can tell me more about your specific application I may be able to offer a more targeted citation. Meanwhile, these papers are good background for microinjection of Morpholinos into embryonic zebrafish.

Eisen JS, Smith JC. Controlling morpholino experiments: don't stop making antisense. Development. 2008 May;135(10):1735-43. Epub 2008 Apr 9.

Robu ME, Larson JD, Nasevicius A, Beiraghi S, Brenner C, Farber SA, Ekker SC. p53 activation by knockdown technologies. PLoS Genet. 2007 May 25;3(5):e78. Epub 2007 Apr 10.

Bill BR, Petzold AM, Clark KJ, Schimmenti LA, Ekker SC. A primer for morpholino use in zebrafish. Zebrafish. 2009 Mar;6(1):69-77.

Moulton JD, Yan YL. Using morpholinos to control gene expression. Curr Protoc Mol Biol. 2008 Jul;Chapter 26:Unit26.8.

Rosen JN, Sweeney MF, Mably JD. Microinjection of zebrafish embryos to analyze gene function. J Vis Exp. 2009 Mar 9;(25). pii: 1115. doi: 10.3791/1115. Open Access Video

Yuan S, Sun Z. Microinjection of mRNA and morpholino antisense oligonucleotides in zebrafish embryos. J Vis Exp. 2009 May 7;(27). pii: 1113. doi: 10.3791/1113.
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Old 01-10-2012, 03:06 PM
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Default Re: Review: Oligonucleotide-based tools for studying zebrafish development.

Thank you sir for the message.

The work that we are trying to do is :

1-Injure the retina of zebrafish.
2-apply cdh2 vivo MO .( how to apply vivo morpholino?)
3-microarray analysis for the change in expression .(microarray analysis seems to be expensive . is there cheaper alternative. how about transcriptome sequencing? is it good enough?)
4-Ontology study.

The main idea was to see the different molecular players associated with cdh 2 during retinal regeneration since cdh2 was shown to be highly up-regulated after injury.


This is our proposed research plan for this semester. Dr. Jon do you think this is good enough work to go on with and what modifications would you recommend to this work .

Sincerely yours
Sunil
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Old 01-16-2012, 04:21 PM
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Default Re: Review: Oligonucleotide-based tools for studying zebrafish development.

You might want to combine steps 1 and 2, delivering the Morpholino during the time of injury. We know that cells are leaky at the time of applied trauma. The Vivo-Morpholinos will enter by endocytosis over time, but it would be better to take advantage of the transient increase in permeability to get some in quickly. That might also allow you to use a lower dose of Vivo-Morpholinos. Vivo-Morpholinos are toxic systemically if the dose is too high. The toxicity has not been much of an issue in local applications, such as what you are suggesting. However, it there is an opportunity to get more knockdown with less oligo it is worth trying.

As for the choice between microarray or transcriptome sequencing, I can't help with that -- I hope someone with experience using both of these can provide a comparison.

Check the Vivo-Morpholino citation list here: [Only registered users see links. ]
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Old 01-20-2012, 03:53 PM
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Default Re: Review: Oligonucleotide-based tools for studying zebrafish development.

Hello Dr. Jon,
Thank you for your help. I wanted to ask you one more thing. i hope i am not disturbing you but i need your help in this.


Can you give me an brief idea as to how pCRII-TOPO vector (Invitrogen) can be used to verify the RT PCR product of my Pcdh17 gene.....thank you so much
Sunil
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Old 01-23-2012, 07:56 PM
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Default Re: Review: Oligonucleotide-based tools for studying zebrafish development.

Hi Sunil,

I've not used that vector. However, if you need to amplify an RT-PCR product by putting it into a vector then transforming bacteria and growing a batch of cloned DNA then this looks like a reasonable choice.
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